Adding the “Art” to STEM

Science, Technology, Engineering and Math = STEM, add “ART” and you get STEAM.

IMG_0359

Cyndi and I in front of some cells

Friday night, I collaborated with my fabulous friend Cyndi Coon for a “STEAM-Y” Ladies night out at Tempe Center for the Arts. Scientists aren’t known for their artistic abilities, but Cyndi has the knack for drawing out the artist in everyone – even me, who insists I’m not a “draw-er.”  The whole evening revolved around creating your own “cell-fie.”

Bringing on the STEM

As the science nerd that I am, I was excited to talk about the connection between how cells look and how they function. In the examples below, you can see how lung cells have little wavy fingers called cilia that are used to remove debris from the lung.  Plant cells have a hard exterior cell wall, which help make plant’s leaves rigid.  They are also green because of the chloroplasts that harness sunlight and turn it into plant energy.  And in the breast, you can see that the cells are organized in such a way that an empty space (called a lumen) is created where breast milk is stored after pregnancy. There are so many cool examples! Pollen. Neurons. Blood cells. The list goes on and on!

What cells look like and how they’re arranged often help to understand how to cell functions

Adding the “A”

Cyndi brought the “STEAM” by talking about Ernst Haeckel who was a PhD trained zoologist turned artist. His illustrations are stunning! Many of his ideas about evolution and biology were later disproved, and he used creative license with many of his “subjects.” However, his art captured a Victorian audience. He was a true scientific communicator (or as Cyndi would say “performance artist”.

It’s from these dual inspirationsIMG_0360 that the thirty or so attendees got to work with their black paper, gel pens, and colored pencils. We were reminded that patterns often occur in nature as does some level of symmetry, which could be used to help us draw our cells. Patterns can be created by grouping shapes together, mimicking groupings of cells. Or you could draw cells so that you can tell from what they look like what the cell might do.

The group was so creative! You can be creative too! Take inspiration from this idea. Why not have your kids or your friends (with a glass of wine) create cellfies? And if you do, share them with me!

cellfies_1

IMG_0366

I can’t encourage you enough to check out Cyndi’s creative work at Laboratory 5 or her speaker page. I love that her transformational talk will encourage you to “channel your naughtiness to expose creativity and use it as a super tool.” 

Read a version of this article with even more info about Ernst Haeckel at GotScience.org

The Reproducibility Problem in Research

recipe

Image credit Pixabay

When you’re baking a cake, you follow a recipe that uses specific ingredients, added in a particular order, mixed in a specific way, and baked for a certain time at an exact temperature. But what if you made the cake twice?  Or three times? Will it be the same each time? Will your cake be “reproducible”? What if your baking powder is old?  The cake might not rise as much as normal.  Or you buy a different brand of flour? What if you’re baking at your sister’s house in Oregon at a higher elevation than normal?  Do you change the time or temperature that the cake bakes? How much? And what if you’re using your Grandmother’s handwritten recipe for her famous spice cake?  It’s filled with phrases such as a “pinch” of cinnamon or “about” 3 cups of flour.  Do you think it will taste the same as when your Grandmother makes it?  And what if two people try to make the same cake? On the Great British Baking Show, one of the challenges each week has each contestant follow the same recipe with the same ingredients to make the same baked item.  They NEVER come out the same because there is variability built until every step, even with the same instructions, equipment, and ingredients.

Science is sometimes a lot like baking.  Instead of a recipe, scientists’ follow a protocol (or standard operating procedure – shortened to “SOP” because scientists like acronyms). We purchase or make ingredients, typically called “reagents.”  Often a single reagent can be bought from many different companies or made in the lab by you or maybe by a technician, or maybe you were in a rush and you borrowed some from someone down the hall. In biology, biological materials like cells or enzymes are often involved.  These could be new or old.  You could have tested and “validated” your cells or antibodies or you could have relied on someone telling you that they are okay. Once you have all of your reagents pulled together, you do the experiment.

Experiments are funny little things.  You follow your SOP, but maybe one day, the 5 minute incubation turns into 10 because you were in the middle of answering an email.  Maybe another day you’re in a rush to get to a seminar so you skip a step.  Or maybe you’re training a new undergraduate how to do the experiment and you let them do a few steps on their own.

This variability is part of the reason why scientists repeat their experiments multiple times. Three, as you may expect, is often the magic number.  These data are then presented (for example, in a grant or a paper) either as a representative experiment, where only one of the three or more experiments are shown, or as an average of the experiments with “error bars” that often show how much the data differed between experiments.  This type of careful presentation gives other researchers more confidence that the result is real, as opposed to something that happened just because the new grad student messed something up.

The Reproducibility “Problem”

However, even with all this careful planning, there is a lot of chatter these days about the failure of scientists to be able to reproduce experiments.  One of the earliest papers about this topic came from researchers at Amgen who found that they couldn’t reproduce 47 out of 53 studies from cancer research labs. This has led to a snowball of studies and reports of the failure to reproduce data from various fields including biology and psychology. The most recent is a Nature Article surveying 1,500 scientists about their  ability to reproduce their own and others’ results in their own labs. 52% of these scientists felt that there was a reproducibility “crisis” and words like “bleak” and “discomfiting” were thrown around to express the severity of the problem.

So is there really a problem? Lots of papers have discussed this already, but I figured why not add my own opinion to the mix.  In part, yes, these likely is a bit of a problem.  This problem stems from using reagents you aren’t sure of.  For example, imagine that you think you’re studying prostate cancer and you think you’re using a cell line from a prostate cancer patient, but actually you’re using a super common cervical cell line? It happens all the time! An effort to make publishers and grantors enforce cell line authentication and other types of reagent confirmation before beginning experiments is gaining steam.  Not a bad idea and not too expensive.

Image credit Pixabay

Image credit Pixabay

Other efforts are also underway where a third party can be “hired” to authenticate results such as the Reproducibility Project. This is expensive, and time consuming, and one might wonder where the value lies in having someone else repeat your experiments? The value lies in having confidence in the result…but as we’ve discussed here already, the minute you move your experiment to another lab with new reagents and new people, you add more variability. If the experiment fails, how do you know it’s because the result was wrong or because someone else did it wrong?

This is where the issue lies, and I think it all comes back to the central goal of science and scientists. Scientists want to uncover what’s really happening in nature. Every experiment is done to test a hypothesis, and these results lead to more experiments and on and on. Even if an experiment doesn’t get identical results each time or can’t be reproduced in another lab, the fundamental question is whether or not the biological hypothesis is correct or not.  No matter what, scientists should always do multiple different kinds of experiments and follow-up experiments to confirm or refute their hypothesis. This all assumes that scientists are ethical and follow the scientific method – as opposed to folks who publish fabricated or modified data just to get a paper published (but that’s a topic for a whole other post!!)

So I guess the question may not be whether or not an experiment is reproducible, but whether or not the hypothesis is true. And if scientists focus on THAT as opposed to reproducibility, per se, then I think science is moving forward in a productive direction!

 

The difference between basic, translational and clinical research

When I started as a researcher, I had no idea that there were different types of research.  I don’t mean that some scientists study cancer and some scientists study Alzheimer’s disease.  I mean entirely different kinds of research that have fundamentally different methods, sources of funding, and purposes. Today’s post is going to outline three main types of research in the biological sciences: basic, translational and clinical research.

Basic Research:

science_image

By en:User:AllyUnion, User:Stannered (en:Image:Science-symbol2.png) [CC BY 3.0 or GFDL], via Wikimedia Commons

 Right off the bat, I need to be super clear that basic research is NOT research that’s easier to do or simpler than any other type of research.  It is just as complex and just as hypothesis-oriented as other types of research.  However, the goal of basic research is to  understand at a very basic level some aspect of biology.  Also called fundamental research, basic research doesn’t require that the outcome of the research can cure a disease or fix a problem.  That being said, basic research often does create the foundation that is required for other researchers to apply to solving a problem. I like how basic research is described on WIkipedia as “Basic research generates new ideas, principles, and theories, which may not be immediately utilized but nonetheless form the basis of progress and development in different fields”  This research can be in biology, physics, math, environmental sciences or any other scientific field. So what are some examples of basic research in biology?

  • Understanding the proteins and pathways that result in cells dying by apoptosis
  • Developing technology to better determine the 3D structure of proteins.
  • Creating mathematical models representing population growth in cities over time
  • Studying how leaf litter affects the ecosystem (an actual active funded grant at TGen here in Arizona)

This research is often funded by the government, specifically the National Institutes of Health, which funds 50,000 grants to more than 300,000 researchers at more than 2,500 institutions around the world, and the National Science Foundation, which funds 24% of all federally-funded basic science research in the United States.

Translational Research:

mouse_for_research

By Maggie Bartlett, NHGRI. [Public domain], via Wikimedia Commons

Translational research is how basic research and biological knowledge is translated into the clinic.  Often called “bench-to-bedside” or research (referring to the research bench and the patient’s bedside) or “applied” research (of applying basic research to solve a real-world problem), this research is needed to show that a drug or device works in some living system before it is used on humans. This is the research that happens after the results from basic research are obtained and before clinical research.

For example, if a drug is found in the lab that targets a protein that is thought to cause a disease like cancer, the drug will first be tested on animal models.  The animal model may be a mouse that has been genetically altered so that it develops that specific kind of cancer or a mouse that has human cancer cells injected into it (like the patient derived xenografts I described in a previous post). The drug will then be used on the animal to see if it is safe or if low doses are so toxic that the animal dies. Whether or not the drug hits the targeted protein or cell type can also be tested in mice.  For example, if the drug is supposed to kill brain tumor cells, researchers would want to make sure the drug was able to pass the blood brain barrier of the mouse.  Finally, if the drug is supposed to kill tumor cells, researchers would want to check that the tumor shrinks, the cells die, and/or that the survival of the mouse is extended from using this treatment. Often, drugs are “weeded out” at the translational research stage saving millions of dollars and years worth of time and effort in clinical trials.

Translational research isn’t just for drug development.  It is also useful for devices. For example, to develop a device that can diagnose diseases in third world countries, where access to electricity and high tech labs is more difficult.

Clinical Research:

blood_tube_for_research

By Tannim101 [CC BY 3.0, GFDL or CC BY 3.0], via Wikimedia Commons

Clinical research is what is performed in a healthcare environment to test the safety and effectiveness of drugs, diagnostic tests, and devices that could be used in the detection, treatment, prevention or tracking of a disease.  The cornerstone of clinical research is the clinical trial.  There are 4 basic phases to a clinical trial.  Each phase is performed sequentially to systematically study the drug or device.

  • Phase I: This is the first time the drug or device has been in humans and it is used on a small number of patients in low doses to see whether or not it is safe and what the side-effects may be. At this point, the clinicians are not trying to determine if the treatment works or not.
  • Phase II: In this phase, more patients are treated with the device or drug to test safety (because more side effects may be identified in a larger, more diverse population) and whether the drug or device is effective (in other words, does it work?).
  • Phase III: This is the phase that focuses on whether the drug or device is effective compared to what is typically already used to treat patients.  It’s used on a large group of people and “end points” like increase in survival or decrease in tumor size are used to evaluate its effectiveness.
  • Phase IV: These trials are done after the drug has gone to market to see if it works in various populations .

There are several different types of clinical trials depending on who is funding them. Some clinical trials can be initiated by a doctor or group of doctors.  These are call “physician-initiated” or “investigator -initiated”  studies and are often used to determine which type of treatment works better in patient care.  For example, there may be two treatments that are commonly used to treat a disease. Investigators may initiate a study to figure out what treatment works better in what patient population.

The kind of clinical research you may be more familiar with are drug companies who are working to develop a drug or device.  These companies will “sponsor” (aka “pay for”) a clinical trial.  They work with clinicians at one or more medical institutes to use their drug or device in a particular way (depending on the phase of the trial) and the clinicians report back the results, including whether there were any side effects to the treatment. At the end of the clinical trial, if the treatment or device was a success, the drug company can apply to the Food and Drug Administration (FDA) for approval to use the drug in the general population.  Bringing a drug to market is a timely and extremely expensive process estimated at over 10 years and $1.3 Billion dollars per drug. Much of this time and cost is due to high cost of conducting the clinical trials.

If you are interested in what clinical trials are currently available in the United States, all clinical trials are registered on ClinicalTrials.gov.  Anyone can search this database to see if trials are available for them to participate in.

Overall, each type of research needs to understand the other, and researchers need to work together to successfully understand our world and to come up with solutions to prevent, diagnose and cure disease.

How do we know the genome sequence?

Imagine someone asked you to explain how a car works. Even if you knew nothing about cars, you could take the car apart piece by piece, inspect each piece in your hand and probably draw a pretty good diagram of how a car is put together.  You wouldn’t understand how it works, but you’d have a good start in trying to figure it out.

Now what if someone asked you to figure out how the genome works? You know it’s made of DNA, but it’s the ORDER of the nucleotides that helps to understand how the genome works (remember genes and proteins?). All the time in the news, you hear about a scientist or a doctor who looked at the sequence of the human genome and from that information could conclude possible causes of the disease or a way to target the treatment. DNA sequencing forms a cornerstone of personalized medicine, but how does this sequencing actually work? How do you take apart the genome like a car so you can start to understand how it works?

As a quick reminder – DNA is made out of four different nucleotides, A, T, G, and C, that are lined up in a specific order to make up the 3 billion nucleotides in the human genome.  DNA looks like a ladder where the rungs are made up of bases that stick to one another: A always sticking to T and G always sticking to C.  Since A always sticks to T and G always sticks to C, if you know the sequence that makes up one side of the ladder, you also know the sequence of the other side.

DNA_ladder

The first commonly used sequencing is called Sanger sequencing, named after Frederick Sanger who invented the method in 1977. Sanger sequencing takes advantage of this DNA ladder – this method breaks it in half and using glowing (fluorescent) nucleotides of different colors, this technique rebuilds the other side of the ladder one nucleotide at a time. A detector that can detect the different fluorescent colors creates an image of these colors that a program then “reads” to give the researcher the sequence of the nucleotides (see image below to see what this looks like).  These sequences are just long strings of As, Ts, Gs, and Cs that the researcher can analyze to better understand the sequence for their experiments.

sanger_sequencing

This was a revolutionary technique, and when the Human Genome Project started in 1990, Sanger Sequencing was the only technique available to scientists. However, this method can only sequence about 700 nucleotides at one time and even the most advanced machine in 2015 only runs 96 sequencing reactions at one time.  In 1990, using Sanger sequencing, scientists planned on running lots and lots of sequencing reaction at one time, and they expected this effort would take 15 years and cost $3 Billion. The first draft of the Human Genome was published in 2000 through a public effort and a parallel private effort by Celera Genomics that cost only $300 million and took only 3 years once they jumped into the ring at 2007 (why was it cheaper and fast, you ask? They developed a fast “shotgun” method and analysis techniques that sped up the process).

As you may imagine, for personalized medicine where sequencing a huge part of the genome may be necessary for every man, woman, and child, 3-15 years and $300M-$3B dollars per sequence is not feasible. Fortunately, the genome sequencing technology advanced in the 1990s to what’s called Next Generation Sequencing. There are a lot of different versions of the Next Gen Sequencing (often abbreviated as NGS), but basically all of them run thousands and thousands of sequencing reactions all at the same time. Instead of reading 700 nucleotides at one time in Sanger sequencing, NGS methods can read up to 3 billion bases in one experiments.

How does this work? Short DNA sequences are stuck to a slide and replicated over and over. This makes dots of the exact same sequence and thousands and thousands of these dots are created on one slide. Then, like Sanger sequencing, glowing nucleotides build the other side of the DNA ladder one nucleotide at a time. In this case though, the surface looks like a confetti of dots that have to be read by a sophisticated computer program to determine the millions of sequencing.

NGS

So what has this new technology allowed scientists to do? It has decreased the cost of sequencing a genome to around $1000. It has also allowed researchers to sequence large numbers of genomes to better understand the genetic differences between people, to better understand other species genomes (including the bacteria that colonize us or the viruses that infect us), and to help determineexomee the genetic changes in tumors to better detect and treat these diseases. Next Generation Sequencing allows doctors to actually use genome sequencing in the
clinic. A version of genome sequencing has been developed called “exome sequencing” that only sequences the genes.  Since genes only make up about 1-2% of the genome, NGS of the exome takes less time and money but provides lots of information about what some argue is the most important part of the genome – the part that encodes proteins.  Much of the promise of personalized medicine can be found through this revolutionary DNA sequencing technique – and with the cost getting lower and lower, there may be a day soon when you too will have your genome sequence as part of your medical record.


For more information about the history of Sequencing, check out this article “DNA Sequencing: From Bench to Bedside and Beyond” in the journal Nucleic Acids Research.

Here is an amusing short video about how Next Generation Sequencing works described by the most interesting pathologist in the world.

Sci Snippet – Do iPhones kill people?

Look at this graph. It’s incredible! As iPhone sales increase from 2007 to 2010, so did the number of deaths caused by people falling down the stairs.  They even increased at the same rate.  It’s crazy – iPhones cause people to die falling down the stairs!!

correlation-causation

For this and other hilarious graphs of silly correlations see tylervigen.com

How obviously ridiculous this is.  Most people could logically deduce that just because iPhone sales and deaths from falling down the stairs “correlate” that one does not “cause” the other. There are lots of other examples (and you can create your own silly correlations) from Spurious Correlations or on other news sites here or here.  And in these cases, you can laugh realizing that just because these two things happen together does not mean that one causes the other.

But even though you’ve probably said that “correlation doesn’t imply causation” or heard someone say it, in science (and science news reporting) the difference is critical to tease out. Why? Understanding if something in science is a cause of the effect you’re seeing can

  • Prevent something harmful from causing damage. For example knowing that smoking is a cause of lung cancer resulted in public health efforts to help people quit smoking.
  • Treat a the cause of a disease or fix the cause of the problem.  For example, knowing that the h.pylori bacteria causes gastritis and ulcers provides a method for treating ulcers by killing the h.pylori. Or if you know that factory waste being dumped into a river or lake causes animal life to die or stop procreating, you can work towards stopping the dumping to save wildlife.
  • Prepare for diseases, outbreaks of disease, or natural disasters.  If you know that earthquakes cause tsunamis, then a warning system can be developed to save people in the tsunami zone.
  • Plan ahead and discuss the possible outcomes from a particular action.  When you know that lack of water in a drought causes dry forest conditions leading to forest fires, you can plan to have greater funding available for fighting these fires in a particularly dry year.
cancer-lung

“Cancer smoking lung cancer correlation from NIH” by Sakurambo – Vectorized version of Image:Cancer smoking lung cancer correlation from NIH.png, originally published on the nih.gov website. The source page has been deleted, but an archived copy is still accessible.Own work, created in Adobe Illustrator. Licensed under Public Domain via Commons

It’s just as important though to tease out when something doesn’t cause an effect – and unfortunately many false claims and pseudoscience is based on taking correlations and touting them as causes.  So how do we figure this out?

In science, a lot of this is determined experimentally and statistically.  In statistics (of which I do not claim to be an expert, but see the links below for more details), the strength of the relationship can be calculated and the stronger the more likely that one causes the other.  The cause/effect relationship should also be tested experimentally, if possible, and the experiment should be repeated to see if the same results are obtained every time.  Without experimental or repeatable experimental results, the relationship is less likely to be causal.  Another interesting measurement is to look at the time frame – if the action takes place months, days, or years apart from the effect, you have to consider whether this would make sense or not.  In the case of smoking and lung cancer, the separation of the two events by years makes sense, but in other cases it may not.  Which also brings up the point of looking at the relationship and thinking about whether or not it makes sense or if a mechanism can be found for the cause and effect relationship.  For example, we know that smoking causes DNA mutations and inflammation which is one of the mechanisms that leads to lung cancer. Alternatively, looking at the iPhone and dying from falling down the stairs example, it’s difficult to find a mechanism that could explain this relationship.

A great description of what to look for comes from the book club book that I’ll be talking about on Thursday, “Bad Science: Quacks, Hacks, and Big Pharma Flacks” by Ben Goldacre with a quote describing evidence-based medicine:

it needs to be a strong association, which is consistent, and specific to the thing you are studying, where the putative cause comes before the supposed effect in time; ideally there should be a biological gradient, such as a dose-response effect; it should be consistent or at least not completely at odds with what is already known (because extraordinary claims require extraordinary evidence); and it should be biologically plausible

Overall, it does come down to the data and some common sense.  If there isn’t any data to support the relationship, you might just be looking at correlation and can confidently holler “iPhones do not kill people!”

To better understand the differences between correlation and causation and the math that can show which you are looking at, check out the Kahn Academy course.  Read more about this topic from Stats with Cats Blog

For more Sci Snippets, click here.

What is that? A beautiful image of deadly tumor cells

the eye

Thanks to Dr. Roberto Fiorelli of Barrow Neurological Institute for sharing this stunning image

It looks like an eye.  Perhaps a terrifying pink eye, like the Eye of Sauron, coming out of the darkness. It’s not an eye, but it is a bit terrifying. This is an image of a slice of the brain showing tumor cells (in green and red) surrounding a blood vessel.  How does this type of image get made?  How does this type of image help scientists? What does it mean that these tumor cells are near a blood vessel?

This image is created with a microscope – specifically a confocal microscope. I’m going to use a very weird analogy to explain why confocal microscopy is so cool, so stick with me. Imagine that you have a jello mold with an object it and you want to know exactly what the object looks like.  Now imagine a regular microscope is like a flashlight.  When you point the flashlight at the jello mold the whole thing lights up including what’s in front of the object, and if the object is translucent, the jello behind the object lights up too.  This gives you an idea of what the object is, but it may be kind of fuzzy because of all the jello you see in front and behind the object.  Confocal microscopy, on the other hand, is designed to turn that wide flashlight beam into a single pinpoint of light so only one part of the object is illuminated at a time.  So when you move this single pinpoint around (back and forth and up and down) over the object, you can get a clear a crisp image of what is inside the jello.

confocal_microscopy

To bring this analogy back into the science-verse, the jello is a cell or a piece of human tissue with layers of many cells.  The objects inside the jello are certain proteins marked so that they light up in different colors (what we call fluorescence) when excited by the light from the laser (flashlight). When confocal microscopy is used to look at these proteins, you can see clear crisp images of exactly where the proteins are in the cells.  And if you take enough images up and down through the cells and the tissue, you can even create a 3D image of the cell or a piece of tissue. Check out this neat video of a 3D rendering of a piece of the brain called the hippocampus.

Now back to the image above.  This is a piece of tissue taken from a patient with an ependymoma, a tumor derived from brain tissue and is primarily found in younger patients.  The colors you see are:

  1. Blue: a chemical called DAPI (or 4′,6-Diamidino-2-Phenylindole, Dihydrochloride) that binds to DNA. Since DNA is found in the nucleus of every cell, staining cells with DAPI helps you to locate each cell in the image – each blue dot is one cell.
  2. Red: stains a protein called GFAP (Glial Fibrillary Acidic Protein) that is found in different cells of the brain, but is also a marker of particular brain tumors, like ependymomas
  3. Green: stains a protein called vimentin that is also found in different cells of the brain, including cells that make up large blood vessels and brain tumors like ependoymomas

So what are we able to learn from this beautiful picture?  See how there are a lot of red and green cells surrounding an empty round space.  That round space is a blood vessel. Cancer cells need food and oxygen to grow, so the green and red cancer cells are clustering around the blood vessel to get the nutrients they need. Even though this is a beautiful image, it helps scientists to understand how these deadly tumors function within the brain and how they find the resources to grow.

If you want to look at more amazing images taken using confocal microscopy and fluorescently tagged proteins, check out these links

Wellcome Image Awards 2015
The Cell: An Image Library

Thanks to Dr. Roberto Fiorelli of Barrow Neurological Institute for sharing this stunning image from his postdoctoral work in Dr. Nadar Sanai’s Laboratory, the Barrow Brain Tumor Research Center

For more “What is That?”, click here.

7 Fun and Interesting Science Websites

I spend a lot of time on my computer; most of my day at work, a few hours when I get home, and every weekend writing this blog and working. Like everyone else, I have high hopes that I’ll focus and power through the day without surfing the web, but I fail miserably every time.  Besides my go-to fluffy news and fun sites (SlateNot Always Working, Dooce), I try, at the very least, to stay on topic and look at science-related website.  Often this means browsing the Table of Contents for hardcore science journals like Nature, Science or Cell, but more often lately, I’m looking at interesting general science websites with stories posted by my scientist friends on Facebook or Twitter. I realize that you, my readers, may not have hundreds of scientist friends regularly sharing  science posts, links and websites with you over social media, so I’ll share some today. Here are seven fun websites that I think you might enjoy.

IFLScience1. I F**king Love Science (IFLScience)

With 21 million followers on Facebook, I’m guessing you’ve heard of this one, but if not, it deserves a follow.  Although there has been some recent controversy about IFLScience posting inaccurate or misleading stories and then failing to correct them, overall this is a fun site that posts multiple times a day about topics from health to space an everything in between.

Ignobel2. Ig Nobel Awards  

Some people wait all year to find out who gets nominated for the Academy Awards and they throw Oscar parties to see who won.  As stereotypical as it may sound, I have that level of excitement for the Nobel Prize announcements. The Nobel website is great, but since I’m guessing you aren’t as obsessed with this yearly event as I am, I’m going to suggest the Ig Nobel Award website instead! Modeled after the Noble Prizes, these awards highlight improbable research that also makes you think. For example, this year the Ig Nobel for Medicine went to researchers in India for treating “uncontrollable” nosebleeds, using the method of nasal-packing-with-strips-of-cured-pork (aka bacon). REALLY FUNNY!

radiolab3. Radiolab

Technically Radiolab is a podcast on NPR, but they do have a website with archives of their podcasts. The two hosts Jad Abumrad and Robert Krulwich are amazing storytellers who focus each of their episodes on a single topic like Sleep or Speed or Sperm. What’s so creative is how they use sound throughout their stories to bring the science to life. I saw them speak about science communication at a meeting, and they ended their presentation with a video that was created based on their episode about Death call Moments. Watch it. It’s incredible.

wired4. Wired Science Section

Wired is a magazine for nerds, and since I’m a total nerd, I love it. vWhat I like the most is that they weave an interesting story without forgoing the important details when dealing with complicated scientific topics, for example, the recent article on the genome editing system CRISPR. I know a lot about CRISPR and genome editing, and I didn’t feel like they watered the topic down, but it was still accessible to a non-scientific audience.

scientificamerican5. Scientific American

One of a few popular science magazines, this is the only one that I look at regularly The articles are fun to read plus in every issue they have a profile of a scientist, which I think is a pretty great way to help people get to know who scientists are as people.  Also, in honor of Jon Stewart leaving the Daily Show (*sigh*), they posted the Top 10 list of  best Science Moments from the show. What’s better than that for Daily Show withdrawal?

NYT6. The New York Times

I love the science section of The New York Times. Matt Ridley (who wrote one of my book club choices Genome), Carl Zimmer and Gina Kolata are only three of many fabulous science journalists who take the time to research a story extraordinarily well providing a real depth and understanding in their pieces.

sciencemag7. News sections for Nature and Science

I know that I said that Nature and Science are hardcore science-for-scientists website, but their News sections hit on the top stories of the week and are more accessible than the science articles.  They also compile in-depth special sections, like the recent “Ebola: Did we Learn?” that has articles about the new Ebola vaccine, what we learned from this ebola pandemic, and how we might respond better next time.

Why did I choose these websites and not others?  Mostly because they were the first that came to mind.  There are thousands of others, and many are listed on the sidebar of this blog. I will also post lists like this every so often so you can get more info about some of these sites.  And please share in the comments your favorite science websites!

Five Ways for You to Participate in Science – Citizen Science

Bunsen_burner

The Bunsen burner I didn’t have. Thanks Wikipedia for the image

I had a chemistry set growing up.  It was small with tiny white bottles holding dry chemicals that sat perfectly on the four tiny shelves of an orange plastic rack.  My dad would let me use the workbench in the basement to do experiments – entirely unsupervised!! You might expect that I did really interesting chemical reactions, and this formative experience helped me to develop into the curious scientist that I am today. Completely wrong.  I remember following the instructions, mixing the chemicals, and then getting stuck because I didn’t have a Bunsen burner.  So many chemical reactions rely on heat, and the green candle stuck to the white plastic top of an aerosol hairspray can wasn’t going to cut it.

My main options for doing science as a kid revolved my failed chemistry experiments, my tiny microscope and slides, and a butterfly net that never netted a single butterfly (not for lack for trying).  However, today with computers (that’s right – no computer growing up – that’s how old I am!) there are hundreds if not thousands of ways for people to get involved in science, without having to invest in a Bunsen burner. This citizen science movement, relies on amateur or nonprofessional scientists crowd-sourcing scientific experiments. I’m talking large scale experiments run by grant-funded university-based scientists that have the possibility of really affecting how we understand the world around us. One example you may have heard about is the now defunct Search for Extraterrestrial Intelligence (SETI) which used people sitting at their computers to analyze radio waves looking for patterns that may be signed of extraterrestrial intelligence. They didn’t find anything, but it doesn’t mean that they wouldn’t have if the program had continued!

Here are five ways that you can become involved in science from where you’re sitting right now!

americangut1. American Gut: Learn about yours (or your dog’s) microbiome

For $99 and a sample of your poop, you will become a participant in the American Gut project. After providing a sample, the scientists will sequence the bacterial DNA to identify all of the bacterial genomes that are present in your gut.  This study already has over 4,000 participants and aims to better understand all of the bacteria that covers and is inside your body – called your microbiome – and to see how the microbiome differs or is similar between different people or between healthy people versus those who may be sick. The famous food writer Michael Pollan wrote about his experience participating this the American Gut project in the New York Times.  They are also looking at dogs and how microbiota are shared with family members, including our pets!

2. Foldit: solve puzzles for sciencefoldit

Puzzles can be infuriating, but at least they have a point to them when you get involved in the Foldit project.  Proteins are the building blocks of life.  Made out of long strings of amino acids, these strings are intricately folded in your cells to make specific 3D shapes that allow them to do their job (like break down glucose to make energy for the cell).  Foldit has you fold structures of selected proteins using tools provided in the game or ones that you create yourself.  These solutions help scientists to better predict how proteins may fold and work in nature.  Over 240,000 people have registered and 57,000 participants were credited in a 2010 publication in Nature for their help in understanding protein structure.  Read more about some of the results here.

3. EyeWire: Mapping the BrainEyeWire-Logo

The FAQs on the EyeWire website are fascinating because as they tell you that there are an estimated 84 billion neurons in the brain, they also insist that we can help map them and their connections. After a brief, easy training, you’re off the the races, working with other people to map the 3D images of neurons in the rat retina.  You win points, there are competitions, and a “happy hour” every Friday night. The goal is to help neuroscientists better understand how neurons connect to one another (the connectome).

4. Personal Genome Project: Understanding pgpyour DNA

The goal of the Personal Genome Project is to create a public database of health, genome and trait data that researchers can then use to better understand how your DNA affects your traits and your health. This project recruits subjects through their website and asks detailed medical and health questions.  Although they aren’t currently collecting samples for DNA sequencing because of lack of funding, they have already sequenced the genomes of over 3,500 participants. The ultimate goal is having public information on over 100,000 people for scientists to use.

mindcrowd5. MindCrowd: Studying memory to understand Alzheimer’s Disease

Alzheimer’s Disease is a disease of the brain and one of the first and most apparently symptoms is memory loss.  MindCrowd wants to start understanding Alzheimer’s disease by first understanding the differences in memory in the normal human brain.  It’s a quick 10 minute test – I took it and it was fun!  They are recruiting an ambitious 1 million people to take this test so that they have a huge set of data to understand normal memory.

This is a randomly selected list based on what I’m interested in and things that I’ve participate in, but you can find a much longer list of projects you can participate in on the Scientific American website or through Wikipedia.  Also, if you’re interested in learning more about the kind of science that people are doing in their own homes, the NY Times wrote an interesting article: Home Labs on the Rise for the Fun of Science.  If decide to try one out, share which one in the comments and what you think!

No s**t?!?! Sharing poop to cure disease – it happens, it works, and here’s why!

I was talking to my sister and four-year-old nephew the other day and my sister prompted him to tell me what he wanted to study when he grew up. He looks right at me and answers “poop”. Totally funny coming from the boy who really is obsessed with his own poop, but as a scientist, I responded that I could tell him lots about poop and asked, “what about poop are you interesting in studying?”  His response, “All of it.” Well, I agree. Poop is far more interesting than we give it credit for.  In this series of posts, I will share with you all the interesting stuff I know about poop. The first post was facts about poop and post is about using poop as a cure for diseases.  Let’s get down and dirty…

gutbalance

Changes in the percentage of different bacterial species in found in patients with various diseases compared to healthy control. From a review in Nature Reviews Microbiology

Your gut is filled with bacteria – estimates of over 100 trillion bacteria – weighing nearly 3 pounds! These bacteria are essential to help digest food and produce vitamins.  These bacteria are also protective against pathogens, like other bad infectious bacteria or viruses.  By studying the proportions of different gut bacterial species, scientists have found that the percentages of these bacterial species is different in patients with various diseases .  Although it isn’t clear if the changes in the gut mircobiome are a cause or consequence of the disease, scientists and clinicians are exploring whether changing the balance of bacteria back to normal can cure (or reduce the symptoms) of these diseases.

cdiff

C. Diff bacteria

In one particular case, it’s clear that a change in the gut microbiome is the cause of the disease and that’s Clostridium Difficile (also known as C. Diff) infection. This infectious bacteria releases toxins that cause mild but annoying symptoms like watery diarrhea 2-3 times per day with abdominal pain or tenderness, but can lead to more severe life-threatening issues like watery diarrhea over 15 times per day or creating a hole in the intestines.  C. Diff is responsible for  ~1% of all hospitalizations per year (>330,000 patients per year) and > 20,000 deaths per year and costs over $3.2 billion dollars for care. The elderly, hospitalized patients or patients taking antibiotics are most at risk for transmission, which is caused by fecal-oral transmission or through hospital workers (since the C. Diff spores aren’t killed by alcohol).

Although an annoying, deadly and expensive disease, C. Diff infection has recently gotten worse.  C. Diff infection is becoming more common and relapse after treatment is more frequent. The bacteria has become more virulent with an increased capacity to produce the symptom-inducing toxins while at the same time becoming resistant to the most common antibiotics used to treat this infection: metronidazole and vancomycin.

So what does this have to do with the microbiome? Well, the normal bacteria in your gut can protect against C. Diff infection.  C. Diff is found in 2-5% of all people who aren’t sick, because the gut microbiome can inhibit C.Diff growth or toxicity directly by making antimicrobial peptides or indirectly by creating an inhospitable environment for C. Diff to grow. Because of this, scientists thought – what if we just fixed the microbiome in C. Diff infected patients so that it’s normal again? And how would they do that? Fecal (POOP) transplant!

poopeatersAlthough you may not be aware, there is a long and storied history of using poop as a treatment – primarily though the eating of poop.  Yes, this is gross, but maybe if we use the official name for eating poop it will sound less gross?  Coprophagy is the consumption of feces, with the distinctions of heterospecific coprophagy being eating feces of other species, allocoprophagy being eating feces of other individuals, and autocoprophagy being eating your own feces. If you have a dog, you know that they love eating poop (their own, cats poop, random poop, all poop really) and so do lots of other animals.   At this point (if I haven’t lost you), you may be wondering why in the world would any animal or person eat poop?? It can help in the  development of the GI tract by helping colonize the gut with bacteria, in developing resistance to pathogens, or in obtaining nutrients. In humans the practice goes back to 300AD in China where fresh, fermented, dried or infant-derived feces, charmingly named “yellow soup”, was used to treat multiple food poisoning or severe diarrhea.  In 1696, Christian Paullini wrote a book on the medical uses of human and animal feces and in 1958 the first modern description of a fecal transplant was described to treat pseudomembranous colitis.

How does fecal transplant work today? The goal is to recolonize the patient’s gut with “normal” gut bacteria.  To get this “normal” gut bacteria, you need a donor. Donors are often family or friends of the patient who are healthy and don’t have any recent antibiotic use.  There is some testing (costing $500-$2000) required to make sure that the poop doesn’t contain particular bacteria or viruses.  Then the poop is prepared for transplant. 50-60 grams of stool is added to a liquid like saline or milk and mixed together in a blender to create a liquid slurry (often patients are requested to provide their own blender). The slurry is then filtered through a coffee filter or metal strainer to remove particulates.

nasolThe feces mix then needs to get into the patient’s gut – and this can be done in a few different ways.

  • Naso-duodenal – from the nose into the stomach using a tube. Although fast and 76% effective, it’s not palatable and often has disgusting side effects like vomiting
  • Transcolonoscopic, which invloves drizzling the fecal mixture out of a colonoscpy tube in the large and small intestines. 89% effective, this method puts the poop directly where it needs to be.
  • Enemas are also highly effective (95%) and are both cheap and safe.  It can be performed at home, but it isn’t recommended.

New methods continue to be developed for fecal transplant to decrease the “gross” factor.  The feces has been dried out and turned into pills.  This is less smelly, but requires ingestion of 24-35 capsules and is more expensive.  Scientists are also trying to culture the correct bacteria mixture in the lab so that a poop donor and poop sample preparation aren’t needed. The best part about this method is that scientists have dubbed it “rePOOPulating” the gut!  Until then, a new business of stool biobanks like OpenBiome are cropping up to meet the need of poop for fecal transplants. For $500, your doctor can request a poop sample for fecal transplant.

For everyone who is completely grossed out right now, it’s important to point out that in patients with C. Diff, this treatment has been over 90% effective in recurrent infections whereas all other treatments were less than 40% effective. Patients are completely on board for this treatment. The biggest issue has been doctors who are grossed out and getting them to use poop to treat these horrible diseases.brownforyou

So next time you look at your poop as you flush it down your toilet, remember how useful poop can be and knowing “what brown can do for you.”

No s**t?!?! Interesting facts about poop

I was talking to my sister and four-year-old nephew the other day and my sister prompted him to tell me what he wanted to study when he grew up. He looks right at me and answers “poop”. Totally funny coming from the boy who really is obsessed with his own poop, but as a scientist, I responded that I could tell him lots about poop and asked, “what about poop are you interesting in studying?”  His response, “All of it.” Well, I agree. Poop is far more interesting than we give it credit for.  In the next two posts, I will share with you all the interesting stuff I know about poop.  This post will be facts about poop and the second post will be about using poop as a cure for diseases.  Let’s get down and dirty...

fecalmatterI’m not one of those people fascinated by poop.  I have never read any of the most popular books on the topic “Everyone Poops” or “What’s Your Poo Telling You“. In fact, I won’t even admit that I poop myself (as my husband will attest I insist that it’s all butterflies and rainbows down there).  But (butt!) being in a lab makes you think about things you never expected.  A common laboratory activity is something called a journal club. Held weekly, undergrads, graduate students and post-docs take turns discussing a scientific topic or journal article.  I like talking about the newest technology and controversial topics, so when it was my turn, I decided to look into the ancient, but recently rediscovered, therapeutic uses of poop to help cure diseases. As a started my research on the topic, I realized that I knew very little about poop in general.  Being the scientist that I am, I went to learn more.  And lucky you, I’m going to share!

watering_poopFirst and foremost, what is poop made of? The majority (75%) is water! The remaining 25% is a mix.  About a third of this 25% (doing the math, that’s 7.5% of your poop) is dead bacteria (back to that later) and a third fiber and undigested food (like those corn kernels you didn’t chew before swallowing).  The final third contains living bacteria, protein, cell linings, fats, salts, and substances released from the intestines and liver. In fact, the brown color of poop comes from some of these secreted substances such as bile and also bilirubin, which comes from dead red blood cells.

seven types of poopThere are seven different types of poop that have been categorized in the Bristol Stool Form Scale (or BSF for short) developed by Dr. Ken Heaton from University of Bristol.  I was going to spend the next 5 minutes wondering exactly what sort of methodology brought him to discover this seven type system, but then I just looked at the original article. “Sixty-six volunteers had their whole-gut transit time (WGTT) measured with radiopaque marker pellets and their stools weighed, and they kept a diary of their stool form on a 7-point scale and of their defecatory frequency.” I’m glad I was not a volunteer in that study – keeping a daily diary of my stool form and have the length of time from mouth to poop tracked – ick!  However, Dr. Heaton was able to conclude that the form the stool takes depends on the time it spends in the colon, with 3 and 4 being ideal stools. Now one more thing for siblings, partners, and spouses to argue about – who’s poo is better?

But(t) let’s get serious.  Besides being an indication of intestinal health, poop is also filled with bacteria.  These bacteria are representative of the bacteria that can be found in your gut and are part of your “microbiome“. Your microbiome (all of the bacteria and other bugs in and around your body) outnumber your human cells 10 to 1, and scientists think that 300-1000 bacterial species inhabit the GI tract alone!  We’re not entirely sure exactly how many species because most of these bacteria don’t grow outside the gut (in the presence of oxygen), and when we look for gut bacteria by sequencing the DNA of poop samples, we’re not sure if the bacteria in poop represents all the bacteria that are found in the gut.

Either way, what do all those bacteria do? They help with digesting food and producing vitamins.  They regulate fat storage and do some crazy things like influence the immune system and the brain (more on that in a future post).  These bacteria are also protective against pathogens, like bad  infectious bacteria or viruses. How the gut microbiome protects against pathogens is still being studied, but we know that some gut microbiome bacteria create antimicrobials that kill bad bacteria.  In other cases, its all about the balance of the good bacteria versus the bad.  When this balance changes, it can be a cause or consequence of the disease. And one of the cures to these diseases, might just be poop itself, which is what I’ll discuss in my next post.

Want to learn more about poop?  Check out some of these resources: